The Abbott government will have to grant $243.5 million to state and territory governments to continue its national schools chaplaincy program after a Queensland father successfully challenged its funding in the High Court.

Prime Minister Tony Abbott reaffirmed his commitment to the program within hours of the High Court’s unanimous decision that federal funding for school chaplains via the Scripture Union of Queensland was unlawful.

Ron Williams took the federal government to the High Court over funding of the school chaplaincy program and won. Photo: Tony Walters

Mr Abbott did not detail how the Coalition would fund it, but said the Coalition "very much support it and we want it to continue".

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Queensland father Ron Williams won his initial challenge against the program two years ago, and won against the government’s law again on Thursday. Mr Williams says there is no place in public schools for non-secular programs.

In the May budget, the Abbott government allocated $243.5 million to continue running the chaplaincy program for another five years. That funding was intended specifically for schools to hire faith-based chaplains rather than social workers.

Four of Mr Williams' children attend a Queensland school that receives federal funding for chaplains.

He said the decision was a huge win for the ''silent majority of parents'' around the country who opposed the chaplaincy program.

Sydney University constitutional law professor Anne Twomey said the federal government would only be able to continue the chaplaincy program by providing grants to state governments rather than directly to chaplains: ''This is the only real option. They can do that and they probably will.”

While the judgement will have a limited impact beyond the chaplaincy program, Professor Twomey said it was still a "slap down" for the federal government.

"This is a reminder from the High Court that the Commonwealth does not have the power it keeps assuming it does - it cannot spend money on whatever it likes.''

National School Chaplaincy Association secretary Peter James said the group expected the Commonwealth to put in place “an alternative funding solution” which could be a system of state and territory grants.

"With the government behind the program and, in fact, bipartisan support for the program, I'm confident that some form of funding will be put in place," he said.

Mr James said funding was guaranteed until December but the federal government would probably need to make changes to the program so that money could flow next year.

Australian Education Union Victorian branch president Meredith Peace said she was opposed to the chaplaincy program in schools.

Schools should have the freedom to hire “qualified professionals” ranging from speech therapists to psychologists.

“I think the decision provides a real opportunity for government to redirect the funding to where it is most needed.”

Ms Peace said the money allocated to the chaplaincy program in the federal budget should also be used to support children with disabilities.

Parents Victoria executive officer Gail McHardy said some schools would be anxious about the future of the program. “Many of our state school families always viewed the chaplains, if their school had one, as providing a complementary role alongside accredited professionals,” she said.

“Parents Victoria wants our schools to have the flexibility to choose and allocate government funding for trained secular counsellors.”

Philip Simpson spends two days a week as chaplain at Blackburn Primary School where he works with children from a range of cultural backgrounds.

He said he provided support to students, their families and teachers.

“I love the job,” he said. “I love the fact that every day I’m there I can make a difference with the kids that I meet.”

Mr Simpson, who has a bachelor’s degree in theology, said he imparted beliefs common to many religions, not just his own Christian faith.

He said forgiveness, acceptance, inclusiveness, grace and unconditional love were values that guided his chaplaincy work.

“It’s not a matter of chaplains being religious gatekeepers. It’s about chaplains being genuine human beings interested in the rights of other people around them.”

In 2012, Mr Williams won his first High Court battle against the chaplaincy program. The Court ruled that it exceeded the Commonwealth's executive spending powers under the constitution.

The judges also said that the government could not spend money on programs that fall outside these powers without authority from Parliament in a law.

About a week later, the then Labor government amended a law to include hundreds of arrangements, grants and programs it could fund. They comprise up to 10 per cent of federal expenditure, including accommodation for asylum seekers offshore and the national counter-terrorism committee.

Mr Williams’ latest High Court challenge held this law was invalid for the payment of the chaplaincy program, which was beyond the Commonwealth's spending powers.

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The Federal Government faces a showdown with some states over whether to allow schools to appoint secular welfare workers instead of chaplains in the wake of the High Court decision that the existing funding agreement is invalid.

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NSW public schools should spend their funding for chaplains on tackling obesity and promoting wellness and positive psychology rather than the untested chaplaincy program which will continue in hundreds of the state's schools, the head of Sydney's Anglican Education Commission has argued.